Clinical and Genomic Characterization of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer: A Multi-institutional Prospective Study

Abstract

Purpose The prevalence and features of treatment-emergent small-cell neuroendocrine prostate cancer (t-SCNC) are not well characterized in the era of modern androgen receptor (AR)-targeting therapy. We sought to characterize the clinical and genomic features of t-SCNC in a multi-institutional prospective study. Methods Patients with progressive, metastatic castration-resistant prostate cancer (mCRPC) underwent metastatic tumor biopsy and were followed for survival. Metastatic biopsy specimens underwent independent, blinded pathology review along with RNA/DNA sequencing. Results A total of 202 consecutive patients were enrolled. One hundred forty-eight (73%) had prior disease progression on abiraterone and/or enzalutamide. The biopsy evaluable rate was 79%. The overall incidence of t-SCNC detection was 17%. AR amplification and protein expression were present in 67% and 75%, respectively, of t-SCNC biopsy specimens. t-SCNC was detected at similar proportions in bone, node, and visceral organ biopsy specimens. Genomic alterations in the DNA repair pathway were nearly mutually exclusive with t-SCNC differentiation ( P = .035). Detection of t-SCNC was associated with shortened overall survival among patients with prior AR-targeting therapy for mCRPC (hazard ratio, 2.02; 95% CI, 1.07 to 3.82). Unsupervised hierarchical clustering of the transcriptome identified a small-cell-like cluster that further enriched for adverse survival outcomes (hazard ratio, 3.00; 95% CI, 1.25 to 7.19). A t-SCNC transcriptional signature was developed and validated in multiple external data sets with > 90% accuracy. Multiple transcriptional regulators of t-SCNC were identified, including the pancreatic neuroendocrine marker PDX1. Conclusion t-SCNC is present in nearly one fifth of patients with mCRPC and is associated with shortened survival. The near-mutual exclusivity with DNA repair alterations suggests t-SCNC may be a distinct subset of mCRPC. Transcriptional profiling facilitates the identification of t-SCNC and novel therapeutic targets.

Trial registration: ClinicalTrials.gov NCT02432001.

Fig 1.

CONSORT diagram indicating biopsy site and disposition for the various analyses. NGS, next-generation sequencing.

Fig 2.

Histologic appearance and immunohistochemical (IHC) staining of the androgen receptor (AR). The top three rows represent biopsy specimens with treatment-emergent small-cell neuroendocrine prostate cancer (t-SCNC) histologic classification. The top two rows have strong 3+ expression of the AR with nuclear localization. The third row demonstrates a t-SCNC biopsy specimen with low (1+) AR nuclear expression. The bottom row represents a metastatic biopsy specimen with typical adenocarcinoma morphology, with 3+ nuclear expression of the AR. Magnification, ×400.

Fig 3.

Transcriptional profile of treatment-emergent small-cell neuroendocrine prostate cancer (t-SCNC). (A) Gene expression analysis identifies t-SCNC cases in unsupervised analysis. Unsupervised hierarchical clustering of transcriptional profile of metastatic castration-resistant prostate cancer biopsy specimens (n = 119). Sample cluster 2 is enriched for presence of t-SCNC histology. The rows show the normalized gene expression of 528 genes with false discovery rate (FDR)-corrected P < .05 for analysis of variance of gene expression in the five sample clusters, k-means clustered with k = 5 (labeled i-v). Hypergeometric testing for gene sets showed the gene clusters are involved in (i) androgen response and metabolic processes; (ii) androgen response, androgen receptor (AR) activity and targets, and FOXA1 network; (iii) translation; (iv) extracellular organization; and (v) cell cycle and transport. Pathology call, AR immunohistochemistry (IHC), and variant calls of TP53 and RB1 shown in top rows. (B) Heatmap showing 61 genes with FDR-corrected P < .05 for t test of gene expression in the t-SCNC–enriched cluster 2 versus all other samples. Genes are k-means clustered, with k = 3 (i-iii), in addition showing genes of interest PEG10, CHGA, E2F1, SYP, and AR (*). Hypergeometric testing for gene set enrichment showed gene cluster i contains genes of the Hallmark E2F Targets gene set, cluster ii is dominated by genes related to androgen response and AR activity, and cluster iii contains genes of the Notch signaling pathway. (C) MARINa-inferred master regulators characterizing gene expression differences between small cell-like cluster versus other clusters. The top 25 most activated (red) and repressed (blue) transcription factors in the small-cell–like cluster samples compared with all other samples are shown, as inferred by the MARINa algorithm (FDR < 0.1). Each transcription factor’s targets are shown as tick marks projected onto the gene expression signature. Each row also shows the regulator’s P value, inferred differential activity (Act), and differential expression (Exp). (D) A newly generated t-SCNC gene expression signature distinguishes small-cell histology with 91% accuracy on leave-pair-out cross-validation. The numerical signature score is directly related to the predicted degree of t-SCNC differentiation (top). The heatmap shows median-centered gene expression of the 106 genes in the signature, and membership in neural system development pathways in column on the right. Abbreviations: NEPC, neuroendocrine prostate cancer.

Fig 4.

Variant calls (point mutations and copy number gain/loss) shown for selected subsets of genes, including androgen receptor (AR), DNA repair pathway, cell cycle, and phosphatidylinositol-3-kinase/mammalian target of rapamycin (PI3K/mTOR) pathway.

Fig 5.

Overall survival from date of metastatic castration-resistant prostate cancer by histologic and genomic subgroups. (A) Overall survival (OS) by histology in the preplanned evaluable cohort of patients with prior abiraterone and/or enzalutamide treatment. Blue line, treatment-emergent small-cell neuroendocrine prostate cancer cohort (t-SCNC); gold line, not t-SCNC cohort (B) Survival by unsupervised transcriptional cluster (cluster 2 v others). Blue line, cluster 2; gold line, other clusters (C) Comparison of survival between cluster 2 cases with t-SCNC histology (blue line) versus cases in other clusters without t-SCNC histology (gold line). HR, hazard ratio.